blocks parameter in plotIndiv with block.spls

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Issue #94 resolved
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Hi, When you use plotIndiv with a block.spls output and you use the parameter blocks, the names associated with each block displayed are not the right.

see code below

## this is the X data as a list of mRNA and miRNA; the Y data set is a single data set of proteins
data = list(mrna = breast.TCGA$data.train$mrna, mirna = breast.TCGA$data.train$mirna)
# set up a full design where every block is connected
design = matrix(1, ncol = length(data), nrow = length(data),
                dimnames = list(names(data), names(data)))
diag(design) =  0
# set number of component per data set
ncomp = c(2)
# set number of variables to select, per component and per data set (this is set arbitrarily)
list.keepX = list(mrna = rep(20, 2), mirna = rep(10,2))
list.keepY = c(rep(10, 2))

TCGA.block.spls = block.spls(X = data, Y = breast.TCGA$data.train$protein,
                             ncomp = ncomp, keepX = list.keepX, keepY = list.keepY, design = design)
# in plotindiv we color the samples per breast subtype group but the method is unsupervised!
plotIndiv(TCGA.block.spls, blocks = c(3,2,1))

Comments (2)

  1. Florian Rohart


    Thanks for your message. There was indeed something wrong with the code. This has now been fixed with commit 598b158. It will be available in the next release. Thanks!

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